1 files changed, 259 insertions, 1 deletions

diff --git a/src/data/shortlist.cpp b/src/data/shortlist.cpp
index 396c6ba4..79d685e0 100644
--- a/src/data/shortlist.cpp
+++ b/src/data/shortlist.cpp
@@ -3,6 +3,8 @@
 #include "marian.h"
 #include "layers/lsh.h"
 
+#include <queue>
+
 namespace marian {
 namespace data {
 
@@ -279,7 +281,9 @@ Ptr<ShortlistGenerator> createShortlistGenerator(Ptr<Options> options,
     std::vector<std::string> vals = options->get<std::vector<std::string>>("shortlist");
     ABORT_IF(vals.empty(), "No path to shortlist given");
     std::string fname = vals[0];
-    if(filesystem::Path(fname).extension().string() == ".bin") {
+    if(isBinaryShortlist(fname)){
+        return New<BinaryShortlistGenerator>(options, srcVocab, trgVocab, srcIdx, trgIdx, shared);
+    } else if(filesystem::Path(fname).extension().string() == ".bin") {
       return New<QuicksandShortlistGenerator>(options, srcVocab, trgVocab, srcIdx, trgIdx, shared);
     } else {
       return New<LexicalShortlistGenerator>(options, srcVocab, trgVocab, srcIdx, trgIdx, shared);
@@ -287,5 +291,259 @@ Ptr<ShortlistGenerator> createShortlistGenerator(Ptr<Options> options,
   }
 }
 
+bool isBinaryShortlist(const std::string& fileName){
+  uint64_t magic;
+  io::InputFileStream in(fileName);
+  in.read((char*)(&magic), sizeof(magic));
+  return in && (magic == BINARY_SHORTLIST_MAGIC);
+}
+
+void BinaryShortlistGenerator::contentCheck() {
+  bool failFlag = 0;
+  // The offset table has to be within the size of shortlists.
+  for(int i = 0; i < wordToOffsetSize_-1; i++)
+    failFlag |= wordToOffset_[i] >= shortListsSize_;
+
+  // The last element of wordToOffset_ must equal shortListsSize_
+  failFlag |= wordToOffset_[wordToOffsetSize_-1] != shortListsSize_;
+
+  // The vocabulary indices have to be within the vocabulary size.
+  size_t vSize = trgVocab_->size();
+  for(int j = 0; j < shortListsSize_; j++)
+    failFlag |= shortLists_[j] >= vSize;
+  ABORT_IF(failFlag, "Error: shortlist indices are out of bounds");
+}
+
+// load shortlist from buffer
+void BinaryShortlistGenerator::load(const void* ptr_void, size_t blobSize, bool check /*= true*/) {
+  /* File layout:
+   * header
+   * wordToOffset array
+   * shortLists array
+   */
+  ABORT_IF(blobSize < sizeof(Header), "Shortlist length {} too short to have a header", blobSize);
+
+  const char *ptr = static_cast<const char*>(ptr_void);
+  const Header &header = *reinterpret_cast<const Header*>(ptr);
+  ptr += sizeof(Header);
+  ABORT_IF(header.magic != BINARY_SHORTLIST_MAGIC, "Incorrect magic in binary shortlist");
+
+  uint64_t expectedSize = sizeof(Header) + header.wordToOffsetSize * sizeof(uint64_t) + header.shortListsSize * sizeof(WordIndex);
+  ABORT_IF(expectedSize != blobSize, "Shortlist header claims file size should be {} but file is {}", expectedSize, blobSize);
+
+  if (check) {
+    uint64_t checksumActual = util::hashMem<uint64_t, uint64_t>(&header.firstNum, (blobSize - sizeof(header.magic) - sizeof(header.checksum)) / sizeof(uint64_t));
+    ABORT_IF(checksumActual != header.checksum, "checksum check failed: this binary shortlist is corrupted");
+  }
+
+  firstNum_ = header.firstNum;
+  bestNum_ = header.bestNum;
+  LOG(info, "[data] Lexical short list firstNum {} and bestNum {}", firstNum_, bestNum_);
+
+  wordToOffsetSize_ = header.wordToOffsetSize;
+  shortListsSize_ = header.shortListsSize;
+
+  // Offsets right after header.
+  wordToOffset_ = reinterpret_cast<const uint64_t*>(ptr);
+  ptr += wordToOffsetSize_ * sizeof(uint64_t);
+
+  shortLists_ = reinterpret_cast<const WordIndex*>(ptr);
+
+  // Verify offsets and vocab ids are within bounds if requested by user.
+  if(check)
+    contentCheck();
+}
+
+// load shortlist from file
+void BinaryShortlistGenerator::load(const std::string& filename, bool check /*=true*/) {
+  std::error_code error;
+  mmapMem_.map(filename, error);
+  ABORT_IF(error, "Error mapping file: {}", error.message());
+  load(mmapMem_.data(), mmapMem_.mapped_length(), check);
+}
+
+BinaryShortlistGenerator::BinaryShortlistGenerator(Ptr<Options> options,
+                                                   Ptr<const Vocab> srcVocab,
+                                                   Ptr<const Vocab> trgVocab,
+                                                   size_t srcIdx /*= 0*/,
+                                                   size_t /*trgIdx = 1*/,
+                                                   bool shared /*= false*/)
+    : options_(options),
+      srcVocab_(srcVocab),
+      trgVocab_(trgVocab),
+      srcIdx_(srcIdx),
+      shared_(shared) {
+
+  std::vector<std::string> vals = options_->get<std::vector<std::string>>("shortlist");
+  ABORT_IF(vals.empty(), "No path to shortlist file given");
+  std::string fname = vals[0];
+
+  if(isBinaryShortlist(fname)){
+    bool check = vals.size() > 1 ? std::stoi(vals[1]) : 1;
+    LOG(info, "[data] Loading binary shortlist as {} {}", fname, check);
+    load(fname, check);
+  }
+  else{
+    firstNum_ = vals.size() > 1 ? std::stoi(vals[1]) : 100;
+    bestNum_ = vals.size() > 2 ? std::stoi(vals[2]) : 100;
+    float threshold = vals.size() > 3 ? std::stof(vals[3]) : 0;
+    LOG(info, "[data] Importing text lexical shortlist as {} {} {} {}",
+        fname, firstNum_, bestNum_, threshold);
+    import(fname, threshold);
+  }
+}
+
+BinaryShortlistGenerator::BinaryShortlistGenerator(const void *ptr_void,
+                                                   const size_t blobSize,
+                                                   Ptr<const Vocab> srcVocab,
+                                                   Ptr<const Vocab> trgVocab,
+                                                   size_t srcIdx /*= 0*/,
+                                                   size_t /*trgIdx = 1*/,
+                                                   bool shared /*= false*/,
+                                                   bool check /*= true*/)
+    : srcVocab_(srcVocab),
+      trgVocab_(trgVocab),
+      srcIdx_(srcIdx),
+      shared_(shared) {
+  load(ptr_void, blobSize, check);
+}
+
+Ptr<Shortlist> BinaryShortlistGenerator::generate(Ptr<data::CorpusBatch> batch) const {
+  auto srcBatch = (*batch)[srcIdx_];
+  size_t srcVocabSize = srcVocab_->size();
+  size_t trgVocabSize = trgVocab_->size();
+
+  // Since V=trgVocab_->size() is not large, anchor the time and space complexity to O(V).
+  // Attempt to squeeze the truth tables into CPU cache
+  std::vector<bool> srcTruthTable(srcVocabSize, 0);  // holds selected source words
+  std::vector<bool> trgTruthTable(trgVocabSize, 0);  // holds selected target words
+
+  // add firstNum most frequent words
+  for(WordIndex i = 0; i < firstNum_ && i < trgVocabSize; ++i)
+    trgTruthTable[i] = 1;
+
+  // collect unique words from source
+  // add aligned target words: mark trgTruthTable[word] to 1
+  for(auto word : srcBatch->data()) {
+    WordIndex srcIndex = word.toWordIndex();
+    if(shared_)
+      trgTruthTable[srcIndex] = 1;
+    // If srcIndex has not been encountered, add the corresponding target words
+    if (!srcTruthTable[srcIndex]) {
+      for (uint64_t j = wordToOffset_[srcIndex]; j < wordToOffset_[srcIndex+1]; j++)
+        trgTruthTable[shortLists_[j]] = 1;
+      srcTruthTable[srcIndex] = 1;
+    }
+  }
+
+  // Due to the 'multiple-of-eight' issue, the following O(N) patch is inserted
+  size_t trgTruthTableOnes = 0;   // counter for no. of selected target words
+  for (size_t i = 0; i < trgVocabSize; i++) {
+    if(trgTruthTable[i])
+      trgTruthTableOnes++;
+  }
+
+  // Ensure that the generated vocabulary items from a shortlist are a multiple-of-eight
+  // This is necessary until intgemm supports non-multiple-of-eight matrices.
+  for (size_t i = firstNum_; i < trgVocabSize && trgTruthTableOnes%8!=0; i++){
+    if (!trgTruthTable[i]){
+      trgTruthTable[i] = 1;
+      trgTruthTableOnes++;
+    }
+  }
+
+  // turn selected indices into vector and sort (Bucket sort: O(V))
+  std::vector<WordIndex> indices;
+  for (WordIndex i = 0; i < trgVocabSize; i++) {
+    if(trgTruthTable[i])
+      indices.push_back(i);
+  }
+
+  return New<Shortlist>(indices);
+}
+
+void BinaryShortlistGenerator::dump(const std::string& fileName) const {
+  ABORT_IF(mmapMem_.is_open(),"No need to dump again");
+  LOG(info, "[data] Saving binary shortlist dump to {}", fileName);
+  saveBlobToFile(fileName);
+}
+
+void BinaryShortlistGenerator::import(const std::string& filename, double threshold) {
+  io::InputFileStream in(filename);
+  std::string src, trg;
+
+  // Read text file
+  std::vector<std::unordered_map<WordIndex, float>> srcTgtProbTable(srcVocab_->size());
+  float prob;
+
+  while(in >> trg >> src >> prob) {
+    if(src == "NULL" || trg == "NULL")
+      continue;
+
+    auto sId = (*srcVocab_)[src].toWordIndex();
+    auto tId = (*trgVocab_)[trg].toWordIndex();
+
+    if(srcTgtProbTable[sId][tId] < prob)
+      srcTgtProbTable[sId][tId] = prob;
+  }
+
+  // Create priority queue and count
+  std::vector<std::priority_queue<std::pair<float, WordIndex>>> vpq;
+  uint64_t shortListsSize = 0;
+
+  vpq.resize(srcTgtProbTable.size());
+  for(WordIndex sId = 0; sId < srcTgtProbTable.size(); sId++) {
+    uint64_t shortListsSizeCurrent = 0;
+    for(auto entry : srcTgtProbTable[sId]) {
+      if (entry.first>=threshold) {
+        vpq[sId].push(std::make_pair(entry.second, entry.first));
+        if(shortListsSizeCurrent < bestNum_)
+          shortListsSizeCurrent++;
+      }
+    }
+    shortListsSize += shortListsSizeCurrent;
+  }
+
+  wordToOffsetSize_ = vpq.size() + 1;
+  shortListsSize_ = shortListsSize;
+
+  // Generate a binary blob
+  blob_.resize(sizeof(Header) + wordToOffsetSize_ * sizeof(uint64_t) + shortListsSize_ * sizeof(WordIndex));
+  struct Header* pHeader = (struct Header *)blob_.data();
+  pHeader->magic = BINARY_SHORTLIST_MAGIC;
+  pHeader->firstNum = firstNum_;
+  pHeader->bestNum = bestNum_;
+  pHeader->wordToOffsetSize = wordToOffsetSize_;
+  pHeader->shortListsSize = shortListsSize_;
+  uint64_t* wordToOffset = (uint64_t*)((char *)pHeader + sizeof(Header));
+  WordIndex* shortLists = (WordIndex*)((char*)wordToOffset + wordToOffsetSize_*sizeof(uint64_t));
+
+  uint64_t shortlistIdx = 0;
+  for (size_t i = 0; i < wordToOffsetSize_ - 1; i++) {
+    wordToOffset[i] = shortlistIdx;
+    for(int popcnt = 0; popcnt < bestNum_ && !vpq[i].empty(); popcnt++) {
+      shortLists[shortlistIdx] = vpq[i].top().second;
+      shortlistIdx++;
+      vpq[i].pop();
+    }
+  }
+  wordToOffset[wordToOffsetSize_-1] = shortlistIdx;
+
+  // Sort word indices for each shortlist
+  for(int i = 1; i < wordToOffsetSize_; i++) {
+    std::sort(&shortLists[wordToOffset[i-1]], &shortLists[wordToOffset[i]]);
+  }
+  pHeader->checksum = (uint64_t)util::hashMem<uint64_t>((uint64_t *)blob_.data()+2,
+                                                        blob_.size()/sizeof(uint64_t)-2);
+
+  wordToOffset_ = wordToOffset;
+  shortLists_ = shortLists;
+}
+
+void BinaryShortlistGenerator::saveBlobToFile(const std::string& fileName) const {
+  io::OutputFileStream outTop(fileName);
+  outTop.write(blob_.data(), blob_.size());
+}
+
 }  // namespace data
 }  // namespace marian